rs2769982

Variant names:

• chr20-49908290-A-G
• rs2769982
• NM_006038.4:c.201T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-49908290-A-G
• chr20-49908290-A-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_006038.4(SPATA2):​c.201T>C​(p.Tyr67Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,614,058 control chromosomes in the GnomAD database, including 197,571 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.42 (15643 hom., cov: 33)
  • Exomes 𝑓: 0.49 (181928 hom.)
• Consequence: SPATA2 NM_006038.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 24 publications found

Genes affected

SPATA2 (HGNC:14681): (spermatogenesis associated 2) Enables signaling receptor complex adaptor activity and ubiquitin-specific protease binding activity. Involved in several processes, including protein deubiquitination; regulation of necroptotic process; and regulation of tumor necrosis factor-mediated signaling pathway. Located in cytoplasm; fibrillar center; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP7: Synonymous conserved (PhyloP=-0.235 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA2	NM_006038.4	c.201T>C	p.Tyr67Tyr	synonymous_variant	Exon 2 of 3	ENST00000289431.10	NP_006029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA2	ENST00000289431.10	c.201T>C	p.Tyr67Tyr	synonymous_variant	Exon 2 of 3	1	NM_006038.4	ENSP00000289431.5
SPATA2	ENST00000422556.1	c.201T>C	p.Tyr67Tyr	synonymous_variant	Exon 2 of 3	2		ENSP00000416799.1

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64172 AN: 152100 Hom.: 15628 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.435

GnomAD2 exomes AF: 0.523 AC: 131543 AN: 251400 AF XY: 0.524

Gnomad AFR exome AF: 0.170

Gnomad AMR exome AF: 0.650

Gnomad ASJ exome AF: 0.364

Gnomad EAS exome AF: 0.782

Gnomad FIN exome AF: 0.595

Gnomad NFE exome AF: 0.471

Gnomad OTH exome AF: 0.514

GnomAD4 exome AF: 0.491 AC: 717206 AN: 1461838 Hom.: 181928 Cov.: 70 AF XY: 0.494 AC XY: 359198 AN XY: 727214

African (AFR) AF: 0.164 AC: 5499 AN: 33478

American (AMR) AF: 0.636 AC: 28449 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 9778 AN: 26136

East Asian (EAS) AF: 0.815 AC: 32372 AN: 39700

South Asian (SAS) AF: 0.607 AC: 52350 AN: 86252

European-Finnish (FIN) AF: 0.596 AC: 31838 AN: 53412

Middle Eastern (MID) AF: 0.400 AC: 2305 AN: 5756

European-Non Finnish (NFE) AF: 0.473 AC: 525869 AN: 1111986

Other (OTH) AF: 0.476 AC: 28746 AN: 60394

GnomAD4 genome AF: 0.422 AC: 64230 AN: 152220 Hom.: 15643 Cov.: 33 AF XY: 0.438 AC XY: 32583 AN XY: 74408

African (AFR) AF: 0.181 AC: 7517 AN: 41562

American (AMR) AF: 0.558 AC: 8536 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3472

East Asian (EAS) AF: 0.786 AC: 4060 AN: 5168

South Asian (SAS) AF: 0.614 AC: 2960 AN: 4824

European-Finnish (FIN) AF: 0.599 AC: 6352 AN: 10602

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32139 AN: 67990

Other (OTH) AF: 0.438 AC: 923 AN: 2108

Alfa AF: 0.440 Hom.: 6715

Bravo AF: 0.404

Asia WGS AF: 0.661 AC: 2296 AN: 3478

EpiCase AF: 0.446

EpiControl AF: 0.445

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.29
DANN	Benign	0.47
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2769982; hg19: chr20-48524827; COSMIC: COSV56868078;